
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   33 (  132),  selected   33 , name T0347AL381_3
# Molecule2: number of CA atoms  196 ( 1574),  selected  196 , name T0347.pdb
# PARAMETERS: T0347AL381_3.T0347.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      I       4           -
LGA    -       -      Y       5           -
LGA    -       -      E       6           -
LGA    -       -      P       7           -
LGA    -       -      R       8           -
LGA    -       -      L       9           -
LGA    -       -      S      10           -
LGA    -       -      R      11           -
LGA    -       -      I      12           -
LGA    -       -      A      13           -
LGA    -       -      I      14           -
LGA    -       -      D      15           -
LGA    -       -      K      16           -
LGA    -       -      L      17           -
LGA    -       -      R      18           -
LGA    -       -      P      19           -
LGA    -       -      T      20           -
LGA    -       -      Q      21           -
LGA    -       -      I      22           -
LGA    -       -      A      23           -
LGA    -       -      V      24           -
LGA    -       -      G      25           -
LGA    -       -      F      26           -
LGA    -       -      R      27           -
LGA    -       -      E      28           -
LGA    -       -      V      29           -
LGA    -       -      E      30           -
LGA    -       -      L      31           -
LGA    -       -      K      32           -
LGA    -       -      R      33           -
LGA    -       -      K      34           -
LGA    -       -      E      35           -
LGA    -       -      W      36           -
LGA    -       -      R      37           -
LGA    -       -      E      38           -
LGA    -       -      T      39           -
LGA    -       -      R      40           -
LGA    -       -      D      46           -
LGA    -       -      F      47           -
LGA    -       -      L      48           -
LGA    -       -      G      49           -
LGA    -       -      N      50           -
LGA    -       -      H      51           -
LGA    -       -      I      52           -
LGA    -       -      V      53           -
LGA    -       -      P      54           -
LGA    -       -      V      55           -
LGA    -       -      V      56           -
LGA    -       -      A      57           -
LGA    -       -      G      58           -
LGA    -       -      P      59           -
LGA    -       -      K      60           -
LGA    -       -      D      61           -
LGA    -       -      R      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      L      65           -
LGA    -       -      I      66           -
LGA    -       -      D      67           -
LGA    -       -      H      68           -
LGA    -       -      H      69           -
LGA    -       -      H      70           -
LGA    -       -      L      71           -
LGA    -       -      V      72           -
LGA    -       -      L      73           -
LGA    -       -      A      74           -
LGA    -       -      L      75           -
LGA    -       -      S      76           -
LGA    -       -      K      77           -
LGA    -       -      E      78           -
LGA    -       -      G      79           -
LGA    -       -      V      80           -
LGA    -       -      E      81           -
LGA    -       -      H      82           -
LGA    -       -      V      83           -
LGA    -       -      L      84           -
LGA    -       -      T      85           -
LGA    -       -      S      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    D     170      A      89          2.057
LGA    R     171      K      90          3.274
LGA    D     172      F      91          3.852
LGA    L     173      S      92           #
LGA    -       -      H      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      K      96           -
LGA    -       -      D      97           -
LGA    -       -      E      98           -
LGA    -       -      F      99           -
LGA    -       -      W     100           -
LGA    L     174      S     101          4.508
LGA    S     175      V     102          3.035
LGA    D     176      M     103          1.300
LGA    S     177      D     104          3.402
LGA    F     178      H     105          2.903
LGA    -       -      R     106           -
LGA    D     179      N     107          2.444
LGA    D     180      L     108          4.819
LGA    A     181      I     109          5.295
LGA    L     182      -       -           -
LGA    A     183      Y     110          1.729
LGA    E     184      P     111          1.945
LGA    A     185      F     112          4.687
LGA    M     186      D     113           -
LGA    -       -      A     114           -
LGA    -       -      Q     115           -
LGA    K     187      G     116          4.294
LGA    L     188      L     117          3.179
LGA    -       -      R     118           -
LGA    -       -      R     119           -
LGA    -       -      Q     120           -
LGA    -       -      S     121           -
LGA    -       -      G     122           -
LGA    -       -      D     123           -
LGA    -       -      I     124           -
LGA    -       -      P     125           -
LGA    -       -      K     126           -
LGA    -       -      N     127           -
LGA    -       -      I     128           -
LGA    -       -      H     129           -
LGA    -       -      D     130           -
LGA    -       -      L     131           -
LGA    -       -      E     132           -
LGA    -       -      D     133           -
LGA    -       -      D     134           -
LGA    -       -      P     135           -
LGA    -       -      F     136           -
LGA    -       -      R     137           -
LGA    -       -      S     138           -
LGA    -       -      L     139           -
LGA    -       -      A     140           -
LGA    -       -      G     141           -
LGA    -       -      A     142           -
LGA    -       -      L     143           -
LGA    -       -      R     144           -
LGA    -       -      M     145           -
LGA    -       -      A     146           -
LGA    -       -      G     147           -
LGA    -       -      G     148           -
LGA    -       -      Y     149           -
LGA    -       -      A     150           -
LGA    -       -      K     151           -
LGA    -       -      V     152           -
LGA    -       -      I     153           -
LGA    -       -      I     154           -
LGA    -       -      P     155           -
LGA    -       -      F     156           -
LGA    -       -      S     157           -
LGA    -       -      E     158           -
LGA    -       -      F     159           -
LGA    -       -      G     160           -
LGA    -       -      W     161           -
LGA    A     189      A     162           #
LGA    K     190      D     163          2.551
LGA    S     191      -       -           -
LGA    R     192      F     164           #
LGA    E     193      L     165          3.859
LGA    A     194      R     166          1.534
LGA    R     195      R     167          4.145
LGA    H     196      R     168          2.072
LGA    L     197      I     169          1.467
LGA    P     198      -       -           -
LGA    G     199      D     170          3.154
LGA    W     200      R     171          2.467
LGA    C     201      -       -           -
LGA    G     202      D     172          1.788
LGA    -       -      L     173           -
LGA    -       -      L     174           -
LGA    -       -      S     175           -
LGA    -       -      D     176           -
LGA    -       -      S     177           -
LGA    -       -      F     178           -
LGA    -       -      D     179           -
LGA    -       -      D     180           -
LGA    -       -      A     181           -
LGA    -       -      L     182           -
LGA    -       -      A     183           -
LGA    -       -      E     184           -
LGA    -       -      A     185           -
LGA    -       -      M     186           -
LGA    -       -      K     187           -
LGA    -       -      L     188           -
LGA    -       -      A     189           -
LGA    -       -      K     190           -
LGA    -       -      S     191           -
LGA    -       -      R     192           -
LGA    -       -      E     193           -
LGA    -       -      A     194           -
LGA    -       -      R     195           -
LGA    -       -      H     196           -
LGA    -       -      L     197           -
LGA    -       -      P     198           -
LGA    -       -      G     199           -
LGA    -       -      W     200           -
LGA    -       -      C     201           -
LGA    -       -      G     202           -
LGA    -       -      V     203           -
LGA    -       -      E     204           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   33  196    5.0     25    3.24     8.00      7.507     0.749

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.659682 * X  +  -0.739917 * Y  +   0.131691 * Z  +  37.612263
  Y_new =   0.205245 * X  +  -0.008804 * Y  +   0.978671 * Z  + -48.238670
  Z_new =  -0.722976 * X  +   0.672641 * Y  +   0.157672 * Z  +   8.517764 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.340546   -1.801046  [ DEG:    76.8076   -103.1924 ]
  Theta =   0.808100    2.333493  [ DEG:    46.3007    133.6993 ]
  Phi   =   2.839960   -0.301633  [ DEG:   162.7177    -17.2823 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0347AL381_3                                  
REMARK     2: T0347.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL381_3.T0347.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   33  196   5.0   25   3.24    8.00   7.507
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL381_3
REMARK Aligment from pdb entry: 1fcyA
ATOM      1  N   ASP   170       9.073  25.110  -0.096  1.00  0.00              
ATOM      2  CA  ASP   170       8.500  26.134  -0.938  1.00  0.00              
ATOM      3  C   ASP   170       8.131  27.391  -0.139  1.00  0.00              
ATOM      4  O   ASP   170       8.494  28.495  -0.549  1.00  0.00              
ATOM      5  N   ARG   171       7.443  27.198   0.974  1.00  0.00              
ATOM      6  CA  ARG   171       7.022  28.291   1.845  1.00  0.00              
ATOM      7  C   ARG   171       6.604  27.732   3.206  1.00  0.00              
ATOM      8  O   ARG   171       5.827  26.800   3.268  1.00  0.00              
ATOM      9  N   ASP   172       7.111  28.307   4.279  1.00  0.00              
ATOM     10  CA  ASP   172       6.643  27.987   5.632  1.00  0.00              
ATOM     11  C   ASP   172       5.713  29.117   6.040  1.00  0.00              
ATOM     12  O   ASP   172       6.086  30.288   6.180  1.00  0.00              
ATOM     13  N   LEU   173       4.446  28.797   6.196  1.00  0.00              
ATOM     14  CA  LEU   173       3.452  29.840   6.407  1.00  0.00              
ATOM     15  C   LEU   173       3.625  30.558   7.738  1.00  0.00              
ATOM     16  O   LEU   173       3.293  31.755   7.781  1.00  0.00              
ATOM     17  N   LEU   174       4.131  29.878   8.756  1.00  0.00              
ATOM     18  CA  LEU   174       4.367  30.586  10.030  1.00  0.00              
ATOM     19  C   LEU   174       5.490  31.617   9.821  1.00  0.00              
ATOM     20  O   LEU   174       5.364  32.729  10.350  1.00  0.00              
ATOM     21  N   SER   175       6.562  31.268   9.093  1.00  0.00              
ATOM     22  CA  SER   175       7.589  32.268   8.839  1.00  0.00              
ATOM     23  C   SER   175       7.049  33.350   7.904  1.00  0.00              
ATOM     24  O   SER   175       7.367  34.535   8.136  1.00  0.00              
ATOM     25  N   ASP   176       6.273  33.023   6.903  1.00  0.00              
ATOM     26  CA  ASP   176       5.686  34.061   6.044  1.00  0.00              
ATOM     27  C   ASP   176       4.847  35.027   6.858  1.00  0.00              
ATOM     28  O   ASP   176       4.931  36.219   6.681  1.00  0.00              
ATOM     29  N   SER   177       4.016  34.530   7.757  1.00  0.00              
ATOM     30  CA  SER   177       3.167  35.440   8.533  1.00  0.00              
ATOM     31  C   SER   177       4.017  36.383   9.341  1.00  0.00              
ATOM     32  O   SER   177       3.758  37.580   9.372  1.00  0.00              
ATOM     33  N   PHE   178       5.058  35.911  10.003  1.00  0.00              
ATOM     34  CA  PHE   178       5.900  36.842  10.751  1.00  0.00              
ATOM     35  C   PHE   178       6.684  37.790   9.854  1.00  0.00              
ATOM     36  O   PHE   178       6.782  38.981  10.167  1.00  0.00              
ATOM     37  N   ASP   179       7.237  37.270   8.759  1.00  0.00              
ATOM     38  CA  ASP   179       8.031  38.085   7.806  1.00  0.00              
ATOM     39  C   ASP   179       7.202  39.227   7.263  1.00  0.00              
ATOM     40  O   ASP   179       7.598  40.378   7.176  1.00  0.00              
ATOM     41  N   ASP   180       5.976  38.866   6.857  1.00  0.00              
ATOM     42  CA  ASP   180       5.120  39.855   6.219  1.00  0.00              
ATOM     43  C   ASP   180       4.642  40.877   7.222  1.00  0.00              
ATOM     44  O   ASP   180       4.505  42.053   6.859  1.00  0.00              
ATOM     45  N   ALA   181       4.380  40.499   8.468  1.00  0.00              
ATOM     46  CA  ALA   181       4.080  41.448   9.515  1.00  0.00              
ATOM     47  C   ALA   181       5.231  42.422   9.767  1.00  0.00              
ATOM     48  O   ALA   181       5.033  43.646   9.895  1.00  0.00              
ATOM     49  N   LEU   182       6.429  41.882   9.829  1.00  0.00              
ATOM     50  CA  LEU   182       7.607  42.721  10.011  1.00  0.00              
ATOM     51  C   LEU   182       7.814  43.640   8.811  1.00  0.00              
ATOM     52  O   LEU   182       8.203  44.814   8.978  1.00  0.00              
ATOM     53  N   ALA   183       7.561  43.173   7.592  1.00  0.00              
ATOM     54  CA  ALA   183       7.647  44.041   6.411  1.00  0.00              
ATOM     55  C   ALA   183       6.659  45.196   6.511  1.00  0.00              
ATOM     56  O   ALA   183       7.034  46.333   6.227  1.00  0.00              
ATOM     57  N   GLU   184       5.389  44.949   6.847  1.00  0.00              
ATOM     58  CA  GLU   184       4.445  46.045   7.046  1.00  0.00              
ATOM     59  C   GLU   184       4.972  47.084   8.011  1.00  0.00              
ATOM     60  O   GLU   184       4.915  48.299   7.791  1.00  0.00              
ATOM     61  N   ALA   185       5.451  46.639   9.168  1.00  0.00              
ATOM     62  CA  ALA   185       5.948  47.579  10.157  1.00  0.00              
ATOM     63  C   ALA   185       7.104  48.415   9.603  1.00  0.00              
ATOM     64  O   ALA   185       7.162  49.611   9.857  1.00  0.00              
ATOM     65  N   MET   186       7.993  47.724   8.867  1.00  0.00              
ATOM     66  CA  MET   186       9.115  48.506   8.267  1.00  0.00              
ATOM     67  C   MET   186       8.700  49.468   7.181  1.00  0.00              
ATOM     68  O   MET   186       9.245  50.532   7.063  1.00  0.00              
ATOM     69  N   LYS   187       7.637  49.105   6.409  1.00  0.00              
ATOM     70  CA  LYS   187       7.107  50.066   5.436  1.00  0.00              
ATOM     71  C   LYS   187       6.660  51.350   6.166  1.00  0.00              
ATOM     72  O   LYS   187       6.969  52.440   5.689  1.00  0.00              
ATOM     73  N   LEU   188       5.957  51.223   7.265  1.00  0.00              
ATOM     74  CA  LEU   188       5.533  52.400   8.022  1.00  0.00              
ATOM     75  C   LEU   188       6.746  53.147   8.516  1.00  0.00              
ATOM     76  O   LEU   188       6.759  54.370   8.442  1.00  0.00              
ATOM     77  N   ALA   189       7.807  52.519   8.967  1.00  0.00              
ATOM     78  CA  ALA   189       9.015  53.187   9.393  1.00  0.00              
ATOM     79  C   ALA   189       9.678  53.882   8.209  1.00  0.00              
ATOM     80  O   ALA   189      10.237  54.981   8.421  1.00  0.00              
ATOM     81  N   LYS   190       9.667  53.326   7.008  1.00  0.00              
ATOM     82  CA  LYS   190      10.252  53.983   5.856  1.00  0.00              
ATOM     83  C   LYS   190       9.456  55.231   5.496  1.00  0.00              
ATOM     84  O   LYS   190      10.037  56.272   5.134  1.00  0.00              
ATOM     85  N   SER   191       8.142  55.202   5.573  1.00  0.00              
ATOM     86  CA  SER   191       7.329  56.384   5.398  1.00  0.00              
ATOM     87  C   SER   191       7.693  57.459   6.427  1.00  0.00              
ATOM     88  O   SER   191       7.863  58.625   6.070  1.00  0.00              
ATOM     89  N   ARG   192       7.855  57.048   7.692  1.00  0.00              
ATOM     90  CA  ARG   192       8.236  57.987   8.763  1.00  0.00              
ATOM     91  C   ARG   192       9.593  58.609   8.482  1.00  0.00              
ATOM     92  O   ARG   192       9.806  59.816   8.669  1.00  0.00              
ATOM     93  N   GLU   193      10.533  57.763   8.051  1.00  0.00              
ATOM     94  CA  GLU   193      11.853  58.244   7.648  1.00  0.00              
ATOM     95  C   GLU   193      11.736  59.285   6.527  1.00  0.00              
ATOM     96  O   GLU   193      12.325  60.362   6.602  1.00  0.00              
ATOM     97  N   ALA   194      10.963  58.908   5.506  1.00  0.00              
ATOM     98  CA  ALA   194      10.807  59.807   4.343  1.00  0.00              
ATOM     99  C   ALA   194      10.304  61.177   4.771  1.00  0.00              
ATOM    100  O   ALA   194      10.815  62.215   4.306  1.00  0.00              
ATOM    101  N   ARG   195       9.320  61.183   5.660  1.00  0.00              
ATOM    102  CA  ARG   195       8.724  62.497   6.044  1.00  0.00              
ATOM    103  C   ARG   195       9.647  63.347   6.879  1.00  0.00              
ATOM    104  O   ARG   195       9.393  64.530   7.027  1.00  0.00              
ATOM    105  N   HIS   196      10.725  62.785   7.400  1.00  0.00              
ATOM    106  CA  HIS   196      11.757  63.536   8.091  1.00  0.00              
ATOM    107  C   HIS   196      12.853  64.052   7.186  1.00  0.00              
ATOM    108  O   HIS   196      13.755  64.764   7.637  1.00  0.00              
ATOM    109  N   LEU   197      12.833  63.671   5.898  1.00  0.00              
ATOM    110  CA  LEU   197      13.844  64.161   4.979  1.00  0.00              
ATOM    111  C   LEU   197      13.514  65.578   4.556  1.00  0.00              
ATOM    112  O   LEU   197      12.402  65.817   4.103  1.00  0.00              
ATOM    113  N   PRO   198      14.448  66.499   4.691  1.00  0.00              
ATOM    114  CA  PRO   198      14.133  67.869   4.344  1.00  0.00              
ATOM    115  C   PRO   198      13.541  68.011   2.926  1.00  0.00              
ATOM    116  O   PRO   198      14.016  67.449   1.958  1.00  0.00              
ATOM    117  N   GLY   199      12.379  68.688   2.931  1.00  0.00              
ATOM    118  CA  GLY   199      11.653  68.993   1.738  1.00  0.00              
ATOM    119  C   GLY   199      10.681  67.946   1.261  1.00  0.00              
ATOM    120  O   GLY   199       9.832  68.216   0.413  1.00  0.00              
ATOM    121  N   TRP   200      10.723  66.720   1.787  1.00  0.00              
ATOM    122  CA  TRP   200       9.890  65.663   1.252  1.00  0.00              
ATOM    123  C   TRP   200       8.409  66.000   1.374  1.00  0.00              
ATOM    124  O   TRP   200       7.612  65.798   0.459  1.00  0.00              
ATOM    125  N   CYS   201       8.012  66.555   2.549  1.00  0.00              
ATOM    126  CA  CYS   201       6.596  66.906   2.753  1.00  0.00              
ATOM    127  C   CYS   201       6.173  68.155   2.009  1.00  0.00              
ATOM    128  O   CYS   201       4.982  68.476   1.949  1.00  0.00              
ATOM    129  N   GLY   202       7.109  68.872   1.400  1.00  0.00              
ATOM    130  CA  GLY   202       6.757  69.942   0.488  1.00  0.00              
ATOM    131  C   GLY   202       6.493  69.482  -0.935  1.00  0.00              
ATOM    132  O   GLY   202       6.019  70.294  -1.752  1.00  0.00              
END
